WASHINGTON -- And we thought replay challenges don't include home runs.

Atlanta Braves manager Fredi Gonzalez got a round-tripper reversed Friday but it wasn't the type of "boundary call" that still is left to umpires' discretion under baseball's new replay rules. And this play adds another set of intracacies to the process.

Nationals shortstop Ian Desmond lined a ball into the left field corner leading off the fifth inning and continued around the bases when Atlanta left fielder Justin Upton threw up his arms because he felt the ball was lodged under the padding along the wall in foul territory.

Gonzalez challenged the ruling of an inside-the-park home run, which was overturned by the New York command center. That put Desmond at second base and he promptly got caught in a rundown between second and third while the next batter was at the plate.

"It just went under the fence and, knowing the rule, you put your hands up," Upton said.

That would be Rule 7.05 (f), which states, in part, that a batter is awarded, "Two bases, if a fair ball … sticks in such fence, scoreboard, shrubbery or vines."

"Sticks" is where this one gets sticky.

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The ball was against the wall in the space between the ground and the bottom of the padding on the wall. The umpires on the field did not stop the play and Desmond kept running.

"I looked in and it didn't look like (third base umpire Marvin Hudson) was coming out to look at it," Upton said. "(Shortstop Andrelton) Simmons was panicking, telling me to throw the ball. I picked it up and threw it."

That's where Nationals manager Matt Williams, whose team ended up losing 2-1, had a problem.

"When he had to, he reached and picked up the ball and threw it in," Williams said. "That was my question. I have a question with that one because of what happened after the fact."

"After the fact" becomes an interesting piece of the puzzle.

Once this call was overturned, it was easy to place Desmond at second. But what if the umpires had immediately agreed with Upton's arms-up signal and stopped Desmond? And Williams challenged and the replay umpires ruled the ball was in play. Would Desmond be allowed to advance to third? To home?

"I knew that I was right," Upton said. "The only thing I was worried about was that I did go in and get the ball. (Hudson) said he can't kill the play until he's 100% sure. The next time, I will stand there and make sure they come out and see it. I should have trusted my instincts. I made it more confusing than it should have been."

So, is there a logical solution?

The amount of space between wall padding and the ground is the crucial element.

Gonzalez said there isn't enough space for a ball under the padding in his home ballpark in Atlanta. Except, he said, "When it's been raining for a few days and the ground gets softer."

Raising the padding so there's clearly more than enough room for a ball carries a bit of danger. A sliding or diving fielder could get his leg jammed into the harder wall under the padding.